Anyway, if we plan to spend a couple nights at a hotel in Rome, does it make sense to buy the cruise transfer or should we arrange private transportation? Not sure I like the train idea (I've heard it's a hassle with luggage, and can be dangerous).

Let me give you short answer here for those that do not want to look on other forums. Yes, its a pain getting from Rome to the port and you only have a few options. The cheapest way is to use the train, but this can be a hassle when you have lots of luggage. You can also take a taxi, have your hotel's concierge arrange for a car/driver, or book transfers on-line. Given the price offered by the cruise line ($150 per person) I would probably opt to simply grab a taxi or have the hotel arrange for transfers. You can easily book transfers from less than 200 Euros per car (some transfer companies will transfer up to 6 for that total price) and you will have the convenience of your own car/taxi without the typcial cruise line transfer delays as they pick-up at multiple locations or wait for stragglers.
As to using the train, if you can handle the luggage you will save a lot of money even if you use taxis at both the Rome and port end of the journey (it is not always easy to get a taxi in Civitavecchia.

Thanks Hank. 200 Euros per car is still $260 in US dollars, so it sounds like we'd need to find another party to really be saving any money. But I do like the idea of using our own private transportation that can accommodate our schedule, vs. waiting for the cruise bus to load up and make multiple stops as you mention, etc.

I guess I need to research a couple transfer companies to see what they charge. Any recommendations?

I thought I read on here that the transfer/shuttle companies were cheaper than taxi's.

We'll be sailing out of Rome again in October. After several cruises and LOTS of investigation we find that when in Rome, using the cruise line transfers is the safest way to insure a pleasant (and timely) arrival at the ship and then back to the airport. Aside from making sure you arrive on time, the quotes we've always received were very little different once you include the requested "tips and tolls"

Other European ports can be easily reached using a taxi, etc., but getting from Rome to Civitavicchia can be a bit of a problem depending on the individual day, traffic, auto accidents, construction, strikes, etc., etc, the list can be endless. Sometimes saving a little money isn't worth it. Ships and planes wait for no one. . .

Good point. We weren't sure we'd be sticking around by the airport though since we're arriving a few days early. Maybe it's worth it to backtrack or catch their transfer that picks up from the city center.

Someone please tell me that the $150 transfer fee is for a round trip. It must be, because otherwise it is $600 dollars per couple to get to the port and back. I can (almost)fly from the US to Rome for that amount!

Of course, on the way back you can probably arrange a group with others and hire a taxi for a somewhat lower fare.